Rapid screening of ancient DNA extracts through uracil detection

Paleogenetic studies provide invaluable insights into past populations. However, the success of ancient DNA retrieval remains difficult to predict. Ancient DNA workflows are time consuming and costly, motivating methods to assess preservation at an early stage. One defining molecular feature of ancient DNA is the accumulation of uracil residues through postmortem cytosine deamination. Here, we leverage a uracil-DNA-specific labeling assay, originally developed for modern DNA, to evaluate whether extracts contain ancient DNA molecules. The assay, which requires only two days to complete, quantifies uracil residues using a uracil-DNA-binding protein and antibody-based labeling. After demonstrating reliable immobilization of short DNA fragments, we applied the assay to twenty archaeological samples spanning diverse contexts. Extracts with the highest inferred uracil contents were more likely to contain ancient DNA, whereas the lowest-ranked extracts were consistently negative. This assay may facilitate early prioritization of promising extracts and deprioritization of samples unlikely to yield informative sequencing data.